The Secrets of Our Past
by SentinelSpockNimoy
Summary: Milo Thatch makes a discovery that leads him to wonder about the past and the vague origins of his new home, Atlantis. As Milo investigates further, he stumbles upon a legacy far older than Atlantis itself and becomes entangled in a struggle spanning hundreds of thousands of years. And amid it all, an old enemy returns to exact revenge on the city...and on the unsuspecting Milo.
1. Prologue

_**I don't own Star Trek, and I don't own Atlantis: The Lost Empire either. I do love them both though. Milo Thatch is an epic nerd!**_

* * *

 **\- 1. Prologue -**

 _This world was the farthest from home the Empire had ever stretched, and it already covered nearly one quarter of the galaxy. But their thirst pushed them to continually expand their borders, to include more worlds in their society. This particular world, third in a series of nine bodies that orbited a central yellow star, was not inhabited by sentient life, but still provided fascinating study opportunities for their scientists and scholars, as well as inspiration for artists and musicians. They could also come here for relaxation once the colony was established._

 _The colony. That's why they were here, to establish their newest colony, the newest part of their vast empire. An empire built not on conquered worlds and battles won, but rather on the expansion and sharing of knowledge and technology. Of course, being the far more advanced civilization they were, they couldn't share EVERYTHING with the peoples they encountered. They knew some of these races would use their technology not to explore and learn as they did, but to destroy and conquer and oppress those who did not possess the technology. As a result, only things like cures for diseases and safer way to obtain resources were shared, as well as languages and history. For those races that had developed space travel, ways to improve their vessels were shared, as well as information about various star systems and areas of the galaxy they had explored._

 _The queen surveyed the area where they had arrived. It was a large island in the middle of an ocean, only accessible by flying in or sailing in on the water. Or possibly swimming, but given the distance between the island and the other landmasses, that was unlikely. Yes, the island would be the perfect place for the colony. It was safe, not easily accessible to others, and easy to defend, as they would be able to see any possible threats well before they reached the island. She sent a message back to her ship, which would then spread it to the small fleet that had come here with her. Already, she heard the sounds of her people and various bits of cargo being transported to the surface from the ships high in orbit. Construction would begin immediately, beginning with the defensive forcefield system and the lifting mechanism that could lower the colony beneath the sea in order to conceal it from detection by orbiting spacecraft_

* * *

 _At long last, the colony was complete. It was a cluster of buildings that resembled a city on their homeworld. They were large and spacious, providing comfortable living spaces for all the people of the colony. One building housed medical facilities, another held science labs, and yet another served as the center of government and home to the archives. Parks and plazas provided beautiful and scenic views enhanced by towering sculptures placed there by skilled artists. Botanists had planted gardens in the parks and now beautiful, colorful plants filled them. Its enormous crystalline power source hovered over it like a miniature sun. The Queen herself had come to personally congratulate all who had made the colony possible. Now that it was fully functional, the studying and exploration of this new world could begin._

* * *

 _Centuries passed and the colony thrived. Its residents carefully and closely observed the ever changing world around them. They watched, fascinated, as new species appeared and others died out. Still others simply changed over time, their features adapting them to the changing environment. One species in particular soon developed into primitive tribal civilizations. They were careful to avoid any contact with these civilizations who were still so primitive they were constantly at war with each other._

 _One day, however, they could not avoid it._

 _A rather flimsy contraption carrying the sentient bipedal organisms washed up on their shores. Being the peaceful people they were, they took pity on the creatures and took them in, expertly nursing them back to health using shards of the power source from above the colony. During this time, they gained more knowledge about the ways of these creatures, learning their primitive language and developing other ways to communicate with them. In return, they provided the creatures with food and places to live, as well as clothing and materials to make their own things with. Over time, the creatures advanced rapidly, and soon forgot their counterparts from off the island. They were content to share the island with the colonists, learning from them and studying with them, becoming a society in themselves. This society called itself "Atlantis" after what the colonists guessed was some deity of theirs, or perhaps it was their name for the power source hovering over the colony, which the creatures seemed to worship. It was understandable why they would, the crystal shards of the power source the creatures wore had greatly extended their life span while also providing them total immunity from disease and even the ability to heal minor injuries instantly. They also sped up the healing of major injuries. Rather than trying to explain the scientific and technological reasons for this to beings who were nowhere near being able to understand it, the colonists were content to just let them see the crystal as some kind of deity or supernatural force. Despite their lack of understanding about how it worked, the creatures quickly developed the ability to utilize he crystal's power through their personal shards, using it to power lights and even their stone vehicles and machines. These machines eventually were upgraded to add defensive capabilities, so they could help the colonists defend themselves if they needed to. Not that either group expected any threat to arise. And for many years, none did._

* * *

 _Neither group saw the catastrophe coming. The colonists, who recognized an attack from orbit, had no time to react, and the Atlanteans had never seen such things. Beams of light raining down from the sky, sweeping all over the island. And yet it was all over in a flash. But the aftermath was devastating._

 _In that one fell attack, all of the colonists had been wiped out, leaving only the Atlanteans, who mourned the loss of those who had been their friends for so long. But even in death, the colonists hadn't forgotten their charges. For in the hand of the colonists' leader was a message to the Atlanteans. Fate had been kind enough to let the message be finished before its creator died. It told the Atlanteans all they needed to know to continue using the power source, and to ensure they didn't run out of resources. It also instructed them on how to use the colony's defensive systems in the event that they needed them. As was their tradition, the Atlanteans cremated the colonists, and scattered their ashes from aboard their flying vehicles._

* * *

 _Generations later, the Atlanteans made the grave error of trying to use the crystal itself as a weapon, resulting in a massive wave the likes of which the planet had never seen before. Panicking, the Queen accepted when the crystal scanned for a volunteer to activate the defensive systems, leaving her tiny daughter behind as she was transported upward and became one with the crystal, thus initiating the defenses. Once they were activated, a forcefield dome covered the island and the enormous crystal. With the protective shield in place, the lifting mechanisms activated, and the island sank into the ocean, disappearing far below as it phase-shifted right through solid rock, into the concealed protective chamber the colonists had carved out long ago when the colony was built. It was safe, but at a cost, for in maintaining the shield for so long against the unforgiving ocean, as well as running the lifting mechanisms and phase shifters, the Queen had expired her own strength and her very life force, her body then becoming fuel for the final parts of the process. Devastated by what his error had caused, the King buried the enormous Crystal beneath his city and silenced all talk about it. As millennia passed, the crystal itself was forgotten, except by the king himself, who would only venture to its chamber to retrieve a shard for a newborn child, an occurrence that became rarer as time passed. Their civilization fell into ruin, a mere shadow of what it used to be. People forgot how to read and write their own language. The great stone flying machines remained grounded, relics from a time long past, their use forgotten. Only knowledge of the healing power of the crystal pendants and the health and longevity they provided remained unchanged. Small lights were the only things the pendants powered now. The city no longer thrived, but it still lived. The people still had enough food and resources to survive and carry on their daily lives without worry. And due to their seclusion beneath the sea, they lived a peaceful existence, free from threats by anyone else, though the king still had giant mechanical guardians created and posted to prevent anyone from coming down and discovering their secret chamber. Thus, Atlantis remained undisturbed._

 _Until the year of 1914, Earth reckoning, when an expedition led by a young linguist finally made it to the sunken colony. The leader of this group was nothing more than a greedy mercenary, out for only himself. He attempted to steal the ancient crystal, despite the warnings and pleas of the linguist, who claimed it would kill the entire city. The outsider had no idea just how right he was. Though he cited various writings and pieces of physical evidence, it was his gut that told him the crystal couldn't be taken. He could somehow sense that the crystal was older than ancient and far more powerful than it appeared, especially when he witnessed it take the princess into itself. The king, realizing too late that he was being repaid for having made another error in his efforts to correct the first, passed his crystal shard on to the linguist, charging him with saving the city and returning the crystal. Even as the dying man spoke, the linguist felt the pull of the crystal's power and had a vague, brief flash of the devastation it could cause on the surface. The flash, together with the crystal's power, penetrated his very being, striking his heart of hearts, igniting a flame he didn't know he had, transforming him from a shy timid boiler operator to a brave warrior. Steeling himself for the likely possibility of death, the linguist had mustered a small armada of his friends and the few warriors Atlantis had. They charged the mercenary head on and engaged his forces in battle, the linguist himself taking on the mercenary, certain he would not survive the encounter._

 _But the crystal protected all of its charges._

 _It passed some of its energy to the linguist when he picked up a shard of the glass it had touched, giving him a burst of new strength, even as the mercenary, now insane with greed and rage as his plans fell apart, grabbed the poor man by his neck and raised an axe in his free hand, preparing to strike the death blow to the linguist. In a last desperate attempt to save himself, the linguist slashed his foe with the crystal shard. The crystal's power combined with the man's rage and greed, completely consuming him. Yet a small part of him remained, enough to chase the linguist up the chain rigging. In a moment of sudden clarity, the linguist threw his entire weight toward the ground, pulling his side of the rigging down with him. Too late did his foe realize the trap as he was lifted upward by the sudden force into the blades that shattered him into glittering dust shards, which rained down breaking the chains and freeing the crystal. With the help of the remainder of the small armada, it was returned to the city in time to activate the defensive forcefield to protect the city from the eruption the battle had caused. At the end of it all, the crystal once again hovered over the colony, and the civilization began to restore its former glory with the help of the linguist-turned-hero, who helped the people reclaim their lost knowledge through his ability to read their language. His reward was the love of the princess, who had been restored by the crystal when it no longer needed her to run the defense system. Together, the two ascended to the throne of the city the linguist had always dreamed of discovering, which he now called home. But his greatest discovery of all was still to come._


	2. In the Old City

_**I don't own Atlantis or Star Trek.**_

* * *

 **\- 2. In the Old City -**

The cool shade of trees welcomed Milo as he ventured into the aptly named Old City, the oldest part of Atlantis at the very center of the city, obscured from view by the thick tree and plant growth that surrounded it. Beneath them, it was dark, as if he were in an actual forest, not the middle of a city. The light from his crystal was enough that he could still see in front of him.

The crystal still felt strange hanging around his neck. Mainly because of where it had come from. Kida's dying father had given it to him when charging him with saving Atlantis and Kida. Despite the words of both father and daughter, Milo still blamed himself for the king's death. He was the one who brought Rourke here, he was the one who pointed Rourke to the king to find the crystal, he was the one that didn't try to help the poor man. And now Kida's father was dead. Because of him. He remembered how he'd cried his eyes out that night, even when Kida came and took him in her arms in an effort to comfort him, he still loosed a waterworks into her shoulder. He'd sobbed his apologies against her, shaking as she held him, running her fingers through his hair and whispering her love in his ear.

He'd finally accepted that neither she, nor the rest of Atlantis, blamed him for the king's death. They blamed Rourke, and praised Milo for slaying him, albeit in a rather unconventional way. The Atlanteans who had been there hadn't been able to wait, immediately telling anyone who would listen about how Milo smote his enemy's ruin in midair above the base of the dormant volcano. The way they told it made him sound like some kind of superhuman hero out of a Greek myth. But Milo didn't see himself that way. He'd just been trying to do the right thing. He hadn't even WANTED to kill Rourke, it just happened. He was just a normal, scrawny little linguist.

 _Ah, but that is the mark of a true hero,_ his grandfather would've said, _One who doesn't consider himself a hero, but says he's just a person doing the right thing._

 _Well, I guess that makes me a hero in your eyes, Grandpa,_ Milo thought _, I just hope I made you proud. After all, I promised you I'd find Atlantis, and I did. I just wish you were here to enjoy it with me._

Milo held the crystal against his heart. The old king had reminded him so much of his grandfather. And now this crystal was all he had to remember the man. The warmth against his skin made him think back to when he was three years old, and the stone faced police officers that had come to the house merely stated loudly that his parents were dead. How he'd dropped the toy he was playing with and started crying, and his grandfather had rushed to his side and hugged him close before picking his tiny grandson up, glaring at the officers who had so coldly shattered the little boy's heart. Bad enough the poor child had been getting picked on for wearing glasses, now add the fact he was orphaned. Thaddeus Thatch had taken him in without a second thought, taking a taxi home to his house in the rain, little Milo clinging to him and crying for a "Mommy and Daddy" that were never coming home the whole time. Thaddeus had loved the little boy like his own son, even as he grew into the skinny yet handsome young man he was now.

A step into nothingness brought Milo out of his thoughts just seconds before he fell in the pool of water. He knew how to swim, so he didn't panic as the dark waters closed around him. He let the water slow his fall before he turned and swam toward the surface. But not before something caught his eye. He surfaced quickly and took a deep breath, then dove back underneath, holding his crystal out in front of him trying to find what he'd seen again. Yes! There it was! It was an opening he'd never noticed before, even though he and Kida had explored these waters already. He surfaced again, took another breath and dove back to the opening. It was barely big enough for him to fit through, and he briefly feared he'd get stuck. But then he was through, and into a large open chamber. The water around him was absolutely clear, allowing the light from his crystal to spread into the room around him. He looked up and saw a rippling surface above him and swam toward it. His head broke through with a splash that echoed off the walls. This room was bigger than he thought. And now that he could see it clearly, the architecture was like nothing he'd ever seen. It was curved, like the ribs of some giant beast, but everything was smooth and even. It had once been brightly colored, he could see, bout he couldn't see anything that would've lit the room. There was no writing anywhere indicating a place to put his crystal. Actually, there was no writing period. Anywhere. Nor were there pictures of any kind on the walls. Milo wondered what purpose the room had served before Atlantis sank.

Suddenly, the hairs on the back of his neck stood up. The water was turning cooler, signaling the coming of night. How long had he been in here? No matter, his decision was made. He would come back here tomorrow. He wanted to know more before he told anyone of the room's existence. He went under again and slithered out the way he'd come in. He hauled himself up out of the pool, wringing out his soaked sash and tunic. before he took off back to the palace where he now lived. He made sure, before he left, to mark the spot where the opening to the room was, although tomorrow he would try to find a way in that didn't involve getting wet. A soft night breeze rustled the plants and Milo shivered, picking up his pace. He couldn't wait to curl up wrapped in a soft, warm blanket with Kida in the palace, and a smile appeared on his face at the mere thought. Finally, every dream he'd ever dreamed as a boy had come true at last


	3. Activation

**_I STILL don't own Atlantis. Seriously, I don't even have the DVD or Blu-ray._**

* * *

 **\- 3. Activation -**

The next day, Milo returned as soon as he could. This time he'd brought a lantern and a firefly globe with him so his crystal wouldn't be his only light. He ran straight into the water and slithered through the hole into the strange room again, holding the globe up out of the water. Now that there was more light, he could see that this was DEFINITELY not Atlantean. For one thing, the colors were off. There was much more red, yellow, and orange, as opposed to the blues and greens of Atlantean styles. Also, the structure itself was strange. The walls were smooth and unadorned, curving outward from floor to ceiling, the columns along the sides following this curve. When he dove down to it, Milo found that the floor was some transparent material on top of intricate sculpted artwork that was about two feet deep. It was the strangest thing he'd ever seen, like something out of the futuristic world of science fiction. Yet Milo sensed that this place was in fact very old, even by Atlantean standards.

He made his way to the other side of the room. Now the water was shallow enough, he could stand on the floor, with the water up to his neck. He slowly walked toward a set of vertical panels, following the outward curve of the walls, that he figured must be a door. Suddenly, as he got close enough to push on them, the panels split at the apex of their curve. There was a loud, groaning and grinding sound as they slid apart, the lower half receding toward the floor the top half toward the ceiling. Both stopped about halfway, grinding to a stop as Milo clambered over them. They groaned shut again as he walked away. But Milo wasn't paying attention to the doors anymore.

He stood at the edge of a large open plaza surrounded by crumbling buildings like the one he'd just left. Even in ruins, they were different from the rest of Atlantis, short and wide and curved on the sides, as opposed to the straight-sided Atlantean structures that were taller and thinner. But what really caught his attention was the huge ring in the center of the plaza with steps on either side, so someone could walk through it. A podium-like structure stood near him, facing the huge ring. Curious, Milo approached it. In the center was a hard dome surrounded by two concentric circles of blocks, a strange symbol in each block. Milo reached out to brush dust off one of them. As soon as his hand touched the symbol, it lit up orange, along with the border of its block. At the same time, the huge ring groaned and part of it spun around until a chevron-shaped structure on it clicked like a lock and lit up orange. Looking closer, Milo realized the ring had all the symbols in a circle around it, and six more chevron structures like the one that had just activated. Figuring it needed all of the chevrons to work, Milo randomly selected six more symbols. Six more chevrons clicked. After the sixth one, the dome in the center of the podium glowed a soft orange. Nervously, for he'd never seen anything like this, Milo placed his hand on the dome. He heard a lock sound as the inside of the ring sprang to life, a cloud of what looked like water shooting outward, then being pulled back in, leaving what looked like a wall of standing water inside the ring.

"Jiminy Christmas!" Milo exclaimed, "What IS this?" He slowly approached and touched the wall of water with his finger. It rippled when he did, but his finger wasn't wet.

 _That's weird,_ he thought. He picked up a small rock and tossed it in. There was no splash, but he saw a brief ripple. But when he went to the other side of the ring, there was no sign of the rock. Suddenly, the wall of water seemed to dissolve in flames, then disappeared entirely, leaving the ring empty as before. Bewildered, Milo started looking for a way out. Seeing the open sky, he now knew he could fly in on a Ketak instead of swimming in. Right now, though, he just had to get back to the palace and tell Kida what he'd found.

* * *

"My lady!" an engineer cried, "A gate has been activated!"

"What? Where?" The queen sprang to her feet.

"The Sol system. Third planet." She leaned over the console as the engineer continued, "It's one of the old ones, ma'am, but it's definitely ours."

"Did anyone pass through?" the queen asked.

"No life forms." said a security officer, approaching them, holding out a small rock, "but this came through. The origin confirms it's one of the old model gates, but since they connect to the new ones as well, we were able to save the address."

"Take that to Science." she ordered, "Have them analyze it to determine if it's safe to travel there."

"My queen, you wish to travel there? Through the old gate?" the engineer questioned.

"I don't have much choice. We need to know who activated the gate and whether or not they're a threat."

"I'll start assembling an away team." the security officer said, "And I'll post guards in case who ever activated the gate tries to come through."

"Good." the queen nodded as the officer left. She turned back to the engineer. "Good work. Keep an eye on that gate. Let me know if it activates again or if any others activate."

"Yes ma'am." The queen stood up and stared out into the stars outside her ship.

 _Was it possible?_ she wondered, _Had one of their colonies survived? But if so, how? Or was someone else controlling the colony now? Had their enemies finally figured out the gate system?_

"Whoever you are," she whispered, "we are coming. And we WILL find you."

* * *

 _ **All right, I know the description of the device sounds like a Stargate. That's because it is. This takes place in my AU based in seasons 1 and 2 of Stargate SG-1 where the Ancients, the guys who built the Stargates, are actually a species from Star Trek (I'm not saying which one, because that's a spoiler for this fic. You'll just have to stay tuned to find out who it is. And if you do know who it is, please don't say who, so as not to ruin the story for others. Thank you very much.**_


End file.
